## [1] "O76_p2_IFNg_R1_2.hicup.bam"

Truncation & Mapping

Truncation Frequency

Category Read 1 Read 2
Total 50,062,192 50,062,192
Not Truncated 29,576,585 29,486,994
Truncated 20,485,607 20,575,198

Truncated Read Length

Category Read 1 Read 2
Average Length Truncated 46.2 47

Mapping Efficiency

Category Read 1 Read 2
Too Short To Map 3,466,681 3,177,920
Unique Alignments 42,923,607 41,770,569
Multiple Alignments 1,609,329 1,705,215
Failed To Align 2,062,575 3,408,488
Paired 36,230,756 36,230,756

Truncation and Mapping Bar Plot

Filtering

Filtering Breakdown by Category

Category Count
Valid Pairs 19,116,826
Invalid Pairs 17,113,930
Same Circularised 78,105
Same Dangling Ends 2,381,099
Same Fragment Internal 8,651,550
Re Ligation 4,830,533
Contiguous Sequence 263,266
Wrong Size 909,377
Total Pairs 36,230,756

Filtering Breakdown Pie Chart

Ditag Length Distribution

Frequency Line Plot

Deduplication

Deduplication Summary Table

Category All Ditags Unique Ditags
Read Pairs 19,116,826 27,918
Cis-close (<10Kbp) 1,824,464 2,667
Cis-far (>10Kbp) 11,797,025 14,940
Trans 5,495,337 10,311

Deduplication Bar Chart

Analysis produced by HiCUP - a tool for mapping and performing quality control on Hi-C data

Babraham Bioinformatics